annotationTable-peakPantheRAnnotation-method: annotationTable accessor

In phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments

annotationTable accessor

Description

annotationTable returns a dataframe (row samples, col compounds) filled with a specific peakTable column

Usage

## S4 method for signature 'peakPantheRAnnotation'
annotationTable(object, column)

Arguments

object	peakPantheRAnnotation
column	a peakTable columns

Value

(data.frame) (row samples, col compounds) filled with a specific peakTable column

Examples

if(requireNamespace('faahKO')){
## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
## compounds

# Paths to spectra files
library(faahKO)
spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
                    system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
                    system.file('cdf/KO/ko18.CDF', package = 'faahKO'))

# targetFeatTable
targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(),
                    c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz',
                    'mzMax'))), stringsAsFactors=FALSE)
targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778,
                        522.2, 522.205222)
targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038,
                        496.2, 496.204962)
targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric,
                                    FUN.VALUE=numeric(2))

annotation <- peakPantheRAnnotation(spectraPaths=spectraPaths,
                                    targetFeatTable=targetFeatTable)

## default values without annotation
annotationTable(annotation)
#                                             ID-1 ID-2
# C:/R/R-3.6.0/library/faahKO/cdf/KO/ko15.CDF   NA   NA
# C:/R/R-3.6.0/library/faahKO/cdf/KO/ko16.CDF   NA   NA
# C:/R/R-3.6.0/library/faahKO/cdf/KO/ko18.CDF   NA   NA
}

phenomecentre/peakPantheR documentation built on Feb. 29, 2024, 9:07 p.m.